The nice thing about VA-API is that once your application targets it then it can take take advantage of all the different sorts of video acceleration out there. Well, that's the idea eventually anyways. So if regardless of what acceleration API you want to use... Gallium3D, OpenCL, VDPAU, XvBA, etc then you can get your acceleration.
If somebody creates any sort of hardware that accelerates what Theora uses then I am sure it could be extended to support that also.
And don't forget that although H.264 is patented, Mythtv, ffmpeg, mplayer, and all that stuff is open source and those codecs are used by pretty much every Linux user in existence that want's to watch any sort of common video format.
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